Results of the GEP-ISFG collaborative study on an X-STR Decaplex
Eduardo Raimondi2008, Forensic Science International: Genetics Supplement Series
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A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group with a PCR multiplex for X chromosome STRs. Markers were selected among those described as polymorphic in humans and that have been used by some laboratories in forensics. Primers and various technical methods were investigated with the aim of optimizing a multiplex for the 10 selected X-STRs. Primer mix stock solutions were sent to the laboratories that were asked to analyse two female bloodstains, taking as reference the genetic profiles from 9947A, 9948 and NA3657 samples. In this work, we report the results obtained by 30 GEP-ISFG laboratories, using this Decaplex, as well as alternative technical conditions that also produced good results.
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Forensic Science International: Genetics Supplement Series 1 (2008) 677–679
www.elsevier.com/locate/FSIGSS
Research article
Results of the GEP-ISFG collaborative study on an X-STR Decaplex
L. Gusmão 1,a,*, C. Alves 1,a, P. Sánchez-Diz 1,b, M.T. Zarrabeitia 1,c, M.A. Abovich 1,d,
I. Aragón 1,e, B. Arce 1,j, G. Arrieta 1,z, E. Arroyo 1,f, I. Atmetlla 1,A, C. Baeza 1,f,
M.C. Bobillo 1,g, L. Cainé 1,h, R. Campos 1,i, L. Caraballo 1,k, E. Carvalho 1,l,
M. Carvalho 1,m, R.M.B. Cicarelli 1,n, D. Comas 1,D, D. Corach 1,g, M. Espinoza 1,z,
M.R. Espinheira 1,o, F. Rendo 1,p, O. Garcı́a 1,q, I. Gomes 1,a,b, A. González 1,r,
A. Hernández 1,s, M. Hidalgo 1,g, P. Lozano 1,e, M. Malaghini 1,t, D. Manzanares 1,r,
B. Martı́nez 1,k, J.A. Martins 1,n, K. Maxzud 1,u, I. Miguel 1,p, N. Modesti 1,u,
M. Montesino 1,v, R. Ortiz 1,w, J.J. Pestano 1,i, M.F. Pinheiro 1,h, L. Prieto 1,v,
E. Raimondi 1,x, J.A. Riancho 1,c, M.B. Rodrı́guez 1,d, I. Salgado 1,y,
N. Salgueiro 1,y, J.J. Sánchez 1,s, S. Silva 1,A, U. Toscanini 1,x, C. Vidales 1,B,
C.V. Silva 1,o, M.C. Villalobos 1,w, C. Vullo 1,C, I. Yurrebaso 1,q,
A.I. Zubillaga 1,B, A. Carracedo 1,b, A. Amorim 1,a
a
IPATIMUP (Institute of Pathology and Molecular Immunology of University of Porto), Portugal
b
Instituto de Medicina Legal, Universidade de Santiago de Compostela, A Coruña, Spain
c
Universidad de Cantabria, Unidad de Medicina Legal and Departamento de Medicina, Spain
d
Banco Nacional de Datos Genéticos, Buenos Aires, Argentina
e
Biologia Molecular Ltda (BIOMOL Ltda), Bogota, Colombia
f
Departamento de Toxicologı́a y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Spain
g
Servicio de Huellas Digitales Genéticos (SHDG) and Cátedra de Genética y Bioquı́mica Molecular, Facultad de Farmacia y Bioquı́mica,
Universidad de Buenos Aires, Argentina
h
Serviço de Genética e Biologia Forense, Delegação do Porto do Instituto Nacional de Medicina Legal, Portugal
i
Laboratorio de Genética Forense, Instituto Anatómico Forense de Las Palma, ULPGC, Islas Canarias, Spain
j
Departamento de Biologı́a, Servicio de Criminalı́stica, Dirección General de la Guardia Civil, Madrid, Spain
k
Laboratorio de Genetica Molecular, Instituto de Investigaciones Inmunologicas de la Universidad de Cartagena, Colombia
l
Laboratório de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
m
Serviço de Genética e Biologia Forense, Delegação de Coimbra, Instituto Nacional de Medicina Legal, Portugal
n
Laboratório de Investigação de Paternidade, Faculdade de Ciências Farmacêuticas, UNESP - Universidade Estadual Paulista,
Araraquara, Brazil
o
Serviço de Genética e Biologia Forense, Delegação de Lisboa. Instituto Nacional de Medicina Legal, Portugal
p
Departamento de Genética, Antropologı́a Fı́sica y Fisiologı́a Animal, Unidad de Secuenciación y Genotipado, Servicio Genómica,
Bizkaia, Univ. Paı́s Vasco (UPV/EHU), Spain
q
Sección de Genética Forense, Area de Laboratorio Ertzaintza, Bizkaia, Spain
r
ADF TecnoGen S.L., Madrid, Spain
s
Instituto Nacional de Toxicologı́a y Ciencias Forenses, Delegación de Canarias, Spain
t
Lab. Frischmann Aisengart SA, Setor de Biologia Molecular, Curitiba, Brazil
u
Laboratório de Biologı́a Molecular do CEPROCOR - Agencia Córdoba Ciencia, Complejo Hospitalario Santa Marı́a de Punilla,
Córdoba, Argentina
v
Comisarı́a General de Policı́a Cientı́fica, Laboratorio de Biologı́a, Madrid, Spain
w
Unidad de Diagnóstico Molecular, Departamento de Bioquı́mica, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
x
PRICAI-Fundación Favaloro, Buenos Aires, Argentina
y
GDPN-Genética Médica e Diagnóstico Pré-Natal Prof. Doutor Sérgio Castedo, S.A. Porto, Portugal
* Corresponding author at: IPATIMUP (Institute of Pathology and Molecular Immunology of University of Porto), Population Genetics, Rua Dr. Roberto Frias s/n,
4200-465 Porto, Portugal. Tel.: +351 225570700; fax: +351 225570799.
E-mail address: [email protected] (L. Gusmão).
URL: http://www.ipatimup.pt
1
On behalf of the GEP-ISFG (The Spanish-Portuguese Working Group of the International Society for Forensic Genetics).
1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.fsigss.2007.10.012
678
L. Gusmão et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 677–679
z
Departamento de Ciencias Forenses, Sección de Bioquı́mica, Unidad de Genética Forense, Poder Judicial, Costa Rica
A
Laboratorio de Análisis Clı́nicos y Moleculares, LACYM S.A. and CIBCM, San José, Costa Rica
B
Unidad de Genética Molecular, Policlı́nica Gipuzkoa, San Sebastián, Spain
C
Laboratorio de Inmunogenética y Diagnóstico Molecular (LIDMO), Córdoba, Argentina
D
Unitat de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
Received 3 September 2007; received in revised form 16 October 2007; accepted 25 October 2007
Abstract
A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group with a PCR multiplex for X chromosome STRs.
Markers were selected among those described as polymorphic in humans and that have been used by some laboratories in forensics. Primers and
various technical methods were investigated with the aim of optimizing a multiplex for the 10 selected X-STRs. Primer mix stock solutions were
sent to the laboratories that were asked to analyse two female bloodstains, taking as reference the genetic profiles from 9947A, 9948 and NA3657
samples. In this work, we report the results obtained by 30 GEP-ISFG laboratories, using this Decaplex, as well as alternative technical conditions
that also produced good results.
# 2008 Elsevier Ireland Ltd. All rights reserved.
Keywords: X-STRs; GEP-ISFG; Multiplex PCR
1. Introduction
2. Material and methods
Many forensic laboratories have recently introduced the
analysis of X-STR markers in their routine, due to the
advantages in the use of these markers in cases of complex
kinship analysis [1,2]. Nevertheless, PCR multiplex strategies, population data, mutation rates and other relevant
genetic information concerning X-STRs are still scarce. In
the last GEP-ISFG quality control (www.gep-isfg.org), in
2006, an increasing number of participating labs (11 out of
116) reported results on the analyses of X-STRs. However,
from the 19 different markers reported, only 6 of them were
typed by, at least, 5 labs (the minimum established by the
GEP for a marker to be evaluated). Moreover, nomenclature
discrepancies were detected in two loci: HPRTB and
DXS8377.
In order to overcome these problems, the GEP decided to
organize a collaborative exercise, consisting on the evaluation of
an X-STR Decaplex including: DXS8378, DXS9898, DXS7133,
GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132,
DXS9902 and DXS6789 (Fig. 1).
Markers were selected taking into account the gene diversity
values reported in different populations; and the potential for
multiplexing. Preference was given to simple rather than
complex STRs, following the ISFG recommendations concerning locus selection for forensic applications [3]. In order to
reduce the potential PCR-generated slippage artifacts, trinucleotide repeats were avoided. To evaluate the optimized multiplex,
primer mix stock solutions were sent to the participating
laboratories and were asked to analyse two female bloodstains,
using the protocol available at www.gep-isfg.org/ISFG/Castel
lano/Grupos_de_trabajo/Cromosomas_sexuales/crx.php.
3. Results and discussion
Of the 30 participating laboratories 23 followed the
proposed amplification protocol. The remaining seven used
alternative methods to perform the multiplex reaction with the
same primer mix. Therefore, instead of the QIAGEN Multiplex
PCR kit (Qiagen), some participants chose to setup the PCR
Fig. 1. Electropherogram of a female profile for the X-STR Decaplex.
L. Gusmão et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 677–679
multiplex using buffers and Taq DNA polymerases already
available in their labs. Namely, three used Taq Gold Polymerase
(Applied Biosystems); two used the Platinum Taq DNA
Polymerase (Invitrogen); one used the Phusion High-Fidelity
DNA Polymerase (BioLabs); and finally one used the Taq
polymerase from Highway Molecular Biology (Argentina).
In spite of the different amplification methods employed, 27
out of the 30 participating laboratories reported identical results
for the 2 control samples for all 10 markers.
Three labs presented different profiles for both control
samples (in several markers), but in all cases the recommended
protocol and/or nomenclature were not followed.
It is worth mentioning that two additional laboratories
correctly typed the control samples in three PCR multiplex
reactions, to allow detection using conventional electrophoresis
and silver-staining techniques.
This newly constructed Decaplex has proved to be
technically very robust since most laboratories successfully
type the distributed samples.
Since population and mutation data are crucial for forensic
evaluation of this new multiplex, and both are lacking for this
set of markers, the next step of this collaborative work will be
data compilation in Iberian and South American populations. In
679
order to assure the quality of results, only the laboratories that
correctly typed the distributed control samples in the first part
of this work (27 out of the 30 participating laboratories) will
collaborate in data collection.
Conflict of interest
None.
References
[1] J. Edelmann, S. Hering, M. Michael, L. Rüdiger, D. Deichsel, G. MeierSundhausen, L. Roewer, I. Plate, R. Szibor, 16 X-chromosome STR loci
frequency data from a German population, Forensic Sci. Int. 124 (2001)
215–218.
[2] S. Hering, Augustin Ch, J. Edelmann, R. Szibor, DXS10079 DXS10074 and
DXS10075 are STRs located within a 280 kb region of Xq 12 and provide
stable haplotypes useful for complex kinship cases, Int. J. Legal Med. 116
(2005) 144–149.
[3] L. Gusmão, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, M.R. Mayr, N.
Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA
Commission of the International Society of Forensic Genetics (ISFG):
an update of the recommendations on the use of Y-STRs in forensic
analysis, Forensic Sci. Int. 157 (2006) 187–197.
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